In the near future, weapons expert James McCullen (Christopher Eccleston) has created a nanotechnology-based weapon capable of destroying an entire city. His company M.A.R.S. sells four warheads to NATO, and NATO troops are tasked with delivering the warheads. Duke (Channing Tatum) and Ripcord (Marlon Wayans) are delivering the warheads when they are ambushed by The Baroness (Sienna Miller), whom Duke recognizes to be his ex-fiancee Ana Lewis. Duke and Ripcord are rescued by Scarlett (Rachel Nichols), Snake Eyes (Ray Park), Breaker (Saïd Taghmaoui) and Heavy Duty (Adewale Akinnuoye-Agbaje). They take the warheads to The Pit, G.I. Joe’s command center in Egypt, and upon arriving rendezvous with the head of The G.I. Joe Team, General Hawk (Dennis Quaid). Hawk takes command of the warheads and excuses Duke and Ripcord, only to be convinced to let them join his group after Duke reveals that he knows The Baroness.

McCullen is revealed to be using the same nanotechnology to build an army of soldiers with the aid of The Doctor (Joseph Gordon-Levitt), planning on using the warheads to cause panic and bring about a new world order. Using a tracking device, McCullen locates The G.I. Joe Base and sends Storm Shadow (Byung Hun-Lee) and The Baroness to retrieve the warheads with assistance from Zartan (Arnold Vosloo). After a fight, Storm Shadow and The Baroness retrieve the warheads and take them to Baron DeCobray, The Baroness’s husband, for him to weaponize. Making their way to Paris, The Joes pursue The Baroness and Storm Shadow but are unsuccessful in stopping them from launching the missile. The nanomites destroy The Eiffel Tower and some of the surrounding area before Duke manages to hit the kill switch, but in doing so he is captured and taken to McCullen’s base under The Arctic.